Welcome to RNAdraw! RNA structure prediction has in the past mainly been
offered only on 'larger' computers due to the 16-bit memory restrictions
implied by MS-DOS. With the Win32 API it is possible to port native 32-bit UNIX
applications to Intel x86 compatible computers without implying any software
based memory and calculation restrictions. Since Win32 is the base of Windows
95, Windows NT and Windows 3.1/3.11 with Win32s, ported programs should be able
to run on an average Windows machine.

Most RNA structure prediction programs have previously had two restrictions:

1. They are available only on 'larger' computers, such as SUN, SGI and IBM
systems.

As you can see, if you have 16 Mb of RAM, you can do up to 1000 bases easily
(remember, the operating system wants some memory too..). On the other hand, if
you lack sufficient memory for you calculations, you can do your calculations
with Rnafold / GCG MFOLD / mfold on a UNIX machine and import
the results into RNAdraw.

Currently there is no installation program for RNAdraw, you will have to
install RNAdraw manually as described in the "install.txt" file included with
RNAdraw.

The sequence window ('RNA Sequences') is the 'control center' of RNAdraw. Here
you see open files and their contents, such as structures and sequences.
Double-clicking on an entry opens the corresponding edit window. As you can see
above, the sequence entry for the first file has been opened. Here you can
edit, cut and paste, import/export RNA
sequences. Double-clicking on the sequence name in the list window opens up a
notepad where you can maintain info about the file. You can for example import
an E-mail into the notepad, cut out a sequence in the mail and paste it into
the sequence editor. From there, you can do your
structure /matrix /heat
calculations and send them to the printer.

One very important concept in RNAdraw is right-button menus. All
windows have an associated right-button menu, so does every entry in the
sequence list. These menus all contain associated data manipulating functions
(more on these below!).

RNAdraw supports 'drag-and-drop'; you can drag a .dra file from the File
Manager/Explorer onto the main window and the file will be opened and added to
the sequence list.

The 'Calculate Structure(s)' menu option is available on the right-button menu
of the sequence entry in the sequence list window. The minimum energy structure
prediction algorithm in RNAdraw was ported from the Rnafold program included in
the Vienna RNA package (1)

This dynamic programming algorithm is based on the work of M. Zuker and P.
Stiegler (2) and uses energy parameters
taken from Turner (3) , Freier
(4) and Jaeger (5) . You can set
multiple temperatures/temperature ranges for structure calculation, easily
enter base-pairing constraints and set other calculation flags. The coordinates
for the returned minimum energy structure are calculated with another ported
program; Naview by R. Bruccoleri (6)
.

Via a toolbar button or main menu option it is possible to modify/save/load all
energy parameters used by the calculational algorithms in RNAdraw. In this way
one can introduce new experimenatlly derived energies, rule out certain
substructural motifs and monitor the effects of energy parameter changes on
subsequently calculated structures.

Under Windows 95 and Windows NT, calculations can be done minimized in the
background.

Above you see two structures in their edit windows. As you can see, you can
adjust which information that will be shown, such as bases, labels, basepairs
etc. You can easily zoom, pan and rotate the viewed structure by pressing the
mouse buttons in different parts of the window, the mouse cursor changes
appropriately to give you some notion of what is going to happen.

The associated right-button menu includes several manipulation functions. For
example, 'Mark Bases' lets you search for and mark sequence tokens in numerous
ways, as you can see in the bottom window where 'UUUU' was used as a token.
'Adjust Basepairs' allows the pairing / unpairing of individual basepairs to
let you inspect structure / energy changes in different conformations.

It is possible to apply basepair probabilities to the structure view, resulting
in thicker lines for higher probabilities, as you can see above.

All structure views can be printed on most Windows printers be exported as
Windows bitmap (.bmp) or metafiles (.wmf/.emf).

The matrix calculation is either done in conjunction with structure calculation
(see Structure Calculation ) or on its
own. The partition function algorithm in RNAdraw was ported from the Rnafold
program included in the Vienna RNA package (1)
.

The matrix calculation is based on work by J.S McCaskill
(7) , the energy parameters are taken from from Turner
(3) , Freier (4) and Jaeger
(5)
. Just as with structure calculation, it is possible to set multiple
temperatures/temperature ranges for matrix calculation, as well as other
calculation flags.

Under Windows 95 and Windows NT, calculations can be done minimized in the
background.

Above to the right you see the basepair-probability matrix of the 37C structure
of the 'Random RNA'. This window can be opened from the 'Open Matrix' menu
option, which is available on the structure view / structure entry right-button
menu. The top right triangle shows the probability matrix, the bottom left
triangle shows the minimum energy structure. As you can see, the probabilities
are grayscale-coded (higher probability = darker gray). Is possible to zoom up
and pan around with the scrollbars, show alignment lines etc.. Moving with the
mouse over the matrix displays the base-pairing probabilities of the underlying
base-pair, as you can see in the status bar.

You can manually pair/unpair basepairs in the structure by clicking with the
left mouse button on a possible basepair in the lower left triangle. If you
have the corresponding structure window open, you can directly monitor
structure changes resluting from your basepair edits.

From the right-button menu of the matrix window you can open the matrix
probability histogram window, which you see above on the bottom left. Here, you
can see the probability frequency distribution of the matrix, print it if you
want to, and set a cutoff frequency for which probabilities are shown in the
matrix.

It is possible to 'extract' structures from the probability matrix, applying
the current cutoff frequency. This allows you to view structures of certain
'probability levels', and compare them with thermodynamically optimal
structures.

Both above windows can be exported and printed in the same manner as with
structure views .

The 'Calculate Heat' menu option is available on the right-button menu of the
sequence entry in the sequence list window. The specific heat calculation
algorithm in RNAdraw was ported from the Rnaheat program included in the Vienna
RNA package (1)
.

The partition function algorithm is based on work by J.S McCaskill
(7) , the energy parameters are taken from Turner
(3) , Freier (4) and Jaeger
(5)
. You are able to set the temperature range and the temperature step value, as
well as other calculation flags.

Under Windows 95 and Windows NT, calculations can be done minimized in the
background (heat calculation can really take some time).

Above you see a Heat window. This window can be opened from the 'Show Heat'
option, which is available on the sequence entry right-button menu. The scroll
bar at the bottom of the window lets you move the above blue marker back and
forth to see individual heat at specific temperatures in the status bar (as
above).

You can print and export the window contents just as with the
structure and matrix windows.

- Any RNA text sequences can be pasted from the clipboard into the sequence
editor.

- GENbank data files can be imported. The whole file will be inserted into the
notepad, the sequence title will be parsed out and the sequence will be
inserted into the sequence editor.

- Rnafold (1)
output files can be used to create new sequence files since they both contain
sequence and structure data. This allows you to do larger calculations on
bigger machines and edit/view them on your PC.

- Rnafold (1)
output files can also be merged with existing sequence files given that both
files designate the same RNA sequence.

- Mulfold .ct files can be imported/merged in the same manner as Rnafold output
files.

- GCG PlotFold -H files containing multiple structures can be imported into
RNAdraw. Each structure will be in its own structure entry in the sequence list

This has been, next to memory requirements, one of the main arguments against
RNA structure prediction on the PC. Nowadays, 486 and especially Pentium
machines deliver lots of calculation power, comparable to the capacity of IBM
AS6000 systems. See the below table for some comparative results. The times
shown are structure calculation/matrix calculation times in seconds.

As you can see, it doesn't take all to long time for smaller sequences on a
486-66DX2 computer, and surprisingly enough, a Pentium-90 outperforms even a
SUN on structure calculation (remember though that this could well be due to
better compiler output, not just processor horsepower).

The implemented version of NAVIEW (6) is
extremly fast; the structure coordinates for a structure with 7250 bases are
calculated within 4 seconds (!) on a 486-66DX2 computer.

I've got lots of plans for RNAdraw, but remember; if nobody seems to be using
the program, I wont do much work on it. You don't have to register to encourage
me, just send me a nice and constructive E-mail and I'll do what I can.

Planned calculation enhancements:

- multiple structure comparison, using both regional and local algorithms

- calculation of suboptimal structures using an improved prediction algorithm

Planned technical enhancements:

- Extended structure coordinate editing

- Modularity : The ability to plug in external algorithms into RNAdraw